Reorder organs for plotting
expr.var.rank.common <- expr.var.common %>%
dplyr::inner_join(expr.rank.first, by="GeneID")
if ("Sex" %in% colnames(filtered.samples$metadata)) {
levels.order <-
c("brain","eye","intestine","liver",
"heart","muscle","gills","pectoral_fin",
"ovary","testis")
} else {
levels.order <-
c("brain","eye","intestine","liver",
"heart","muscle","gills","pectoral_fin","gonads")
}
# Exclude missing conditions from factor levels
levels.exclude <- setdiff(levels.order, levels(as.factor(expr.var.rank.common$Tissue)))
# Reorder levels for plotting
expr.var.rank.common$Tissue <-
factor(expr.var.rank.common$Tissue, levels=levels.order, exclude=levels.exclude)
Density plots
Variability rank vs. mean expression
density_plot_variability_vs_mean(expr.var.rank.common, title=params$species.name)

Mean expression vs. tau
density_plot_mean_vs_tau(expr.var.rank.common, title=params$species.name)

Residual variation vs. tau
density_plot_resid_var_vs_tau(expr.var.rank.common, title=params$species.name)

Variability rank vs. tau
density_plot_variability_vs_tau(expr.var.rank.common, title=params$species.name)
